Next-generation sequencing is rapidly becoming the method of choice for the analysis of RNA, such as for transcriptional profiling. In contrast to microarray technology, sequencing allows identification of novel transcripts and does not require preexisting knowledge of the sequence of the genome. In addition, unlike hybridization-based detection, the sequencing of RNA allows genome-wide analysis of transcription at single nucleotide resolution.
Despite progress, sequencing of specific strands of RNA remains cumbersome and expensive. What is needed is an inexpensive method of sequencing large numbers of RNA simultaneously in solution. The method must be rapid and easy to perform. Methods of simultaneously sequencing large numbers of RNA molecules would provide chemical screens of cell cultures to identify drugs of interest, tissue, blood and other biological sample bank screening. These methods further would allow screening of RNA from tissue in paraffin-blocks. These methods would also provide antibiotic screening to determine drug resistance in microorganisms. This disclosure meets that need.